Evolution Research - General Evolution News

General Evolution News Category of the 'Evolution Research - Main Blog' website: News reports, associated technical papers, authors' homepages, and other relevant information.

Monday, March 05, 2007

Evolutionary history of vespid wasps rewritten by New study

Scientists at the University of Illinois have conducted a genetic analysis of vespid wasps that revises the vespid family tree and challenges long-held views about how the wasps' social behaviors evolved. In the study [1], published in the February 21, 2007 Proceedings of the National Academy of Sciences journal, the researchers found genetic evidence that eusociality (the reproductive specialization seen in some insects and other animals) evolved independently in two groups of vespid wasps.

These findings contradict an earlier model of vespid wasp evolution, which placed the groups together in a single lineage with a common ancestor.

Eusocial behavior is quite rare, and generally involves the breeding of different reproductive classes within a colony. The sterile members of the group perform tasks that support their fertile counterparts. Eusociality occurs in only a few species of insects, rodents, crustaceans and other arthropods.

The evolution of eusociality in wasps has long been a source of debate, said U. of I. entomology graduate student Heather Hines and entomology professor Sydney Cameron, who is the principal investigator of the study. A prior model of vespid wasp evolution placed three subfamilies of wasps - the Polistinae, Vespinae and Stenogastrinae - together in a single evolutionary group with a common ancestor. This model did not rely on a genetic analysis of the wasps, but instead classified them according to several physical and behavioral traits.

Cameron's team included University of Missouri biology professor James H. Hunt, an expert on the evolution of social behavior in the vespid wasps. Hunt observed that many behavioral characteristics of the vespid wasps contradicted this model of the vespid family tree.

Hunt's observations, along with those of other behavioral experts in the field, prompted the new analysis.

Instead of affirming a linear, step-wise evolution of social behavior from solitary to highly social, Cameron said, her team's analysis shows that the Polistinae and Vespinae wasp subfamilies evolved their eusocial characteristics separately from the eusocial Stenogastrinae subfamily of vespid wasps.

Experts on vespid wasp behavior have long noted the significant behavioral differences between the Stenogastrinae subfamily and the group that includes Polistinae and Vespinae. And others have tried, unsuccessfully, to challenge the earlier non-genetic model of vespid wasp evolution. In 1998, German researchers J. Schmitz and R. Moritz also used a genetic analysis to propose that the subfamily Stenogastrinae was evolutionarily distinct from the Polistinae and Vespinae subfamilies.

Proponents of the non-genetic model criticized their work, however, because it relied on an analysis of less than 600 base pairs from two genes (one ribosomal RNA, the other mitochondrial DNA) and included very few representative species, some of which were unsuitable for the analysis.

The new study examined variations in fragments of four genes across 30 species of vespid wasps. Four independent statistical analyses tested the reliability of the pattern of relationships that emerged from the data.

This work confirms the ideas of Schmitz and Moritz, said Cameron, by adding to the weight of evidence that their hypothesis was accurate.

The fact that eusociality evolved independently in two groups of vespid wasps also sheds light on the complexity of evolutionary processes, Cameron said.

"Scientists attempt to make generalizations and simplify the world. But the world isn't always simple and evolution isn't simple. This finding points to the complexity of life."

Eusocial wasps of the family Vespidae are thought to have derived their social behavior from a common ancestor that had a rudimentary caste-containing social system. In support of this behavioral scenario, the leading phylogenetic hypothesis of Vespidae places the eusocial wasps (subfamilies Stenogastrinae, Polistinae, and Vespinae) as a derived monophyletic clade, thus implying a single origin of eusocial behavior. This perspective has shaped the investigation and interpretation of vespid social evolution for more than two decades. Here we report a phylogeny of Vespidae based on data from four nuclear gene fragments (18S and 28S ribosomal DNA, abdominal-A and RNA polymerase II) and representatives from all six extant subfamilies. In contrast to the current phylogenetic perspective, our results indicate two independent origins of vespid eusociality, once in the clade Polistinae+Vespinae and once in the Stenogastrinae. The stenogastrines appear as an early diverging clade distantly related to the vespines and polistines and thus evolved their distinctive form of social behavior from a different ancestor than that of Polistinae+Vespinae. These results support earlier views based on life history and behavior and have important implications for interpreting transitional stages in vespid social evolution.

In this new assessment of the empirical evidence, an alternative to the standard model is proposed: group selection is the strong binding force in eusocial evolution; individual selection, the strong dissolutive force; and kin selection (narrowly defined), either a weak binding or weak dissolutive force, according to circumstance. Close kinship may be more a consequence of eusociality than a factor promoting its origin. A point of no return to the solitary state exists, as a rule when workers become anatomically differentiated. Eusociality has been rare in evolution, evidently due to the scarcity of environmental pressures adequate to tip the balance among countervailing forces in favor of group selection. Eusociality in ants and termites in the irreversible stage is the key to their ecological dominance and has (at least in ants) shaped some features of internal phylogeny. Their colonies are consistently superior to solitary and preeusocial competitors, due to the altruistic behavior among nestmates and their ability to organize coordinated action by pheromonal communication.

In eusociality, an evolutionarily advanced level of colonial existence, adult colonial members belong to two or more overlapping generations, care cooperatively for the young, and are divided into reproductive and nonreproductive (or at least less-reproductive) castes. The phenomenon is well marked and nearly confined to insects, especially ants, bees, wasps, and termites, where it has been subject to a large body of mostly specialized research scattered across disciplines from genetics to paleontology. It has long been the conviction of researchers on social insects that common principles exist at the organismic and superorganismic levels, thus between individual insects and the tightly integrated colonies they compose. Parallels have been persuasively drawn between the self-construction of organisms from molecules and tissues and that of superorganisms from interacting entire organisms. The principles can be further parsed into two segments of the time scale: the developmental decision rules that assemble organisms and colonies in each generation and the origin of these rules through evolutionary time.

Focusing here on the second principle, evolutionary process, we suggest how three seemingly disparate evolutionary phenomena can be causally linked: the selection forces that generate and shape eusociality, the rareness of the origin of eusociality, and the ecological hegemony of eusocial insects.

Climate - and not modern humans - was the cause of the Neanderthal extinction in the Iberian Peninsula (Cave Art). Such is the conclusion of the University of Granada research group RNM 179 - Mineralogy and Geochemistry of sedimentary and metamorphic environments, headed by professor Miguel Ortega Huertas and whose members Francisco Jose Jimenez Espejo, Francisca Martínez Ruiz and David Gallego Torres work jointly at the department of Mineralogy and Petrology of the University of Granada (Universidad de Granada) and the Andalusian Regional Institute of Earth Sciences (CSIC-UGR).

The results of this multidisciplinary research are an important contribution to the understanding of the Neanderthal extinction and the colonisation of the European continent by Homo Sapiens.

During the last Ice Age, the Iberian Peninsula was a refuge for Neanderthals, who had survived in local pockets during previous Ice Ages, bouncing back to Europe when weather conditions improved.

Climate reconstructions

The study is based upon climate reconstructions elaborated from marine records and using the experience of Spanish and international research groups on Western Mediterranean paleoceanography. The conclusions point out that Neanderthal populations did suffer fluctuations related to climate changes before the first Homo Sapiens arrived in the Iberian Peninsula. Cold, arid and highly variable climate was the least favourable weather for Neanderthals and 24,000 years ago they had to face the worst weather conditions in the last 250,000 years.

The most important about these data is that they differ from the current scientific paradigm which makes Homo Sapiens responsible for the Neanderthal extinction. This work is a contribution to a new scientific current - leaded by Dr. Clive Finlayson, from the Gibraltar Museum - according to which Neanderthal isolation and, possibly, extinction were due to environmental factors.

These studies on climate variability are part of the work of the group RNM 179, funded by the excellence project RNM 0432 of the Andalusian Regional Government's Department for Innovation, Science and Business and by the MARCAL project of the Spanish Ministry of Education and Science, both linked to the Andalusian Environment Centre (CEAMA - Centro Andaluz de Medio Ambiente).

Source (adapted): University of Granada PR "Spanish scientists point at climate changes as the cause of the Neanderthal extinction in the Iberian Peninsula" February 25 2007 [alt. Neandertal, Neandertals]

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[1] Based on the paper:

Climate forcing and Neanderthal extinction in Southern Iberia: insights from a multiproxy marine record

Paleoclimate records from the western Mediterranean have been used to further understand the role of climatic changes in the replacement of archaic human populations inhabiting South Iberia. Marine sediments from the Balearic basin (ODP Site 975) was analysed at high resolution to obtain both geochemical and mineralogical data. These data were compared with climate records from nearby areas. Baexcces was used to characterize marine productivity and then related to climatic variability. Since variations in productivity were the consequence of climatic oscillations, climate/productivity events have been established. Sedimentary regime, primary marine productivity and oxygen conditions at the time of population replacement were reconstructed by means of a multiproxy approach. Climatic/oceanographic variations correlate well with Homo spatial and occupational patterns in Southern Iberia. It was found that low ventilation (U/Th), high river supply (Mg/Al), low aridity (Zr/Al) and low values of Baexcess coefficient of variation, may be linked with Neanderthal hospitable conditions. We attempt to support recent findings which claim that Neanderthals populations continued to inhabit southern Iberia between 30 and approx 28 ky cal BP and that this persistence was due to the specific characteristics of South Iberian climatic refugia. Comparisons of our data with other marine and continental records appear to indicate that conditions in South Iberia were highly inhospitable approx 24 ky cal BP. Thus, it is proposed that the final disappearance of Neanderthals in this region could be linked with these extreme conditions.

"It's not just whether you eat insects, fruit, nectar or candy bars or where you eat them -- it matters how reliable that food source is from day-to-day," said W. Alice Boyle. "For example, some really long-distance migrants like arctic terns are not fruit-eaters."

Boyle, an adjunct lecturer in UA's department of ecology and evolutionary biology and co-author Courtney J. Conway, a UA assistant professor of natural resources and a research scientist with the U.S. Geological Survey, reported their findings in the March 2007 issue of American Naturalist [1].

To figure out the underlying pressures that drive some birds to leave home for the season, the team wanted to examine a related set of species and compare their size, food type, habitat, migratory behavior and whether they fed in flocks.

Having the tree let the researchers compare a variety of traits across the many species of Tyranni by using a computer analysis called phylogenetic independent contrasts.

The technique allowed the scientists to sort out whether a bird was migratory because that's what species on their side of the family tree always did or whether the bird's travel habits had some ecological correlates.

Food scarcity was the number one issue that predicted a species' migratory behavior, the team found. Boyle said, "Food availability is the underlying process, not diet and habitat."

One strategy for dealing seasonal changes in food availability is migration. The team also found that species that forage in flocks are less likely to migrate.

"If you are faced with food scarcity, you have two options," Boyle said. "You can either forage with other birds or you can migrate."

When birds band together to search for food, the group is more likely to find a new patch of food than is one lone individual, she said. "Flocking can be an alternative way to deal with food shortages."

A universal assumption about bird migration has been that short-distance migration is an evolutionary stepping stone to long-distance migration. The team's work contradicts that idea by showing that short-distance migrants are inherently different from their globe-trotting cousins.

The question of why birds migrate is still poorly understood despite decades of debate. Previous studies have suggested that use of edge habitats and a frugivorous diet are precursors to the evolution of migration in Neotropical birds. However, these studies did not explore other ecological correlates of migration and did not control for phylogeny at the species level. We tested the evolutionary precursor hypothesis by examining the extent to which habitat and diet are associated with migratory behavior, using a species-level comparative analysis of the Tyranni. We used both migratory distance and sedentary versus migratory behavior as response variables. We also examined the influences of foraging group size, membership in mixed-species flocks, elevational range, and body mass on migratory behavior. Raw species analyses corroborated some results from studies that put forth the evolutionary precursor hypothesis, but phylogenetically independent contrast analyses highlighted an important interaction between habitat and diet and their roles as precursors to migration. Foraging group size was consistently associated with migratory behavior in both raw species and independent contrast analyses. Our results lead to a resource variability hypothesis that refines the evolutionary precursor hypothesis and reconciles the results of several studies examining precursors to migration in birds.

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A 2006 related paper:

Phylogenetic tests of hypotheses for the evolution of avian migration: a case study using the Motacillidae

The evolution of avian migration continues to be an intriguing research subject, even though relationships between migration and factors such as seasonality clearly exist. The question remains whether these relationships are evident within phylogenies containing both sedentary and migratory taxa. We explore the evolution of migration in the family Motacillidae by evaluating existing hypotheses for the evolution of migration in a comparative, phylogenetic framework at the interspecific level. Many hypotheses to explain the evolution of avian migration - such as the "evolutionary precursor" hypothesis (Levey and Stiles 1992, Chesser and Levey 1998) and the "stepping-stone" hypothesis (Cox 1968, 1985) - are based on New World migratory systems. The central components of these hypotheses should apply across biogeographic realms (i.e. the Old World), given that seasonality and habitat regimes are similar in the New and Old worlds. Using a molecular phylogeny containing most species in the Motacillidae, we investigated the potential interactions of seasonality and ecology with migratory and sedentary behavior. Our results suggest that habitat and migration are not correlated in the manner predicted by the evolutionary precursor hypothesis, but they also suggest the importance of increasing seasonality in explaining the patterns of the evolution of migration, an expected but previously unexamined evolutionary relationship. While understanding the limitations of applying generalizations to a complex evolutionary system such as migration, we have delineated here a broad methodology for testing hypotheses about the evolution of migration within a phylogenetic context.

Thursday, March 01, 2007

Genes and Genius: Confirmation of association between Gene and Intelligence

A team of scientists, led by psychiatric geneticists at Washington University School of Medicine in St. Louis, has gathered the most extensive evidence to date that a gene that activates signaling pathways in the brain influences one kind of intelligence. They have confirmed a link between the gene, CHRM2, and performance IQ, which involves a person's ability to organize things logically.

"This is not a gene for intelligence," says Danielle M. Dick, Ph.D., assistant professor of psychiatry and lead author on the study. "It's a gene that's involved in some kinds of brain processing, and specific alterations in the gene appear to influence IQ. But this single gene isn't going to be the difference between whether a person is a genius or has below-average intelligence."

Dick's team comprehensively studied the DNA along the gene and found that several variations within the CHRM2 gene could be correlated with slight differences in performance IQ scores, which measure a person's visual-motor coordination, logical and sequential reasoning, spatial perception and abstract problem solving skills. When people had more than one positive variation in the gene, the improvements in performance IQ were cumulative. The study's findings are available online in Behavioral Genetics and will appear in an upcoming print issue of that journal [1].

IQ tests also measure verbal skills and typically include many subtests. For this study, subjects took five verbal subtests and four performance subtests, but the genetic variations influenced only performance IQ scores.

"One way to measure performance IQ may be to ask people to order pictures correctly to tell a story," Dick explains. "A simple example might be pictures of a child holding a vase, the vase broken to bits on the floor and the child crying. The person taking the test would have to put those pictures into an order that tells the story of how the child dropped the vase and broke it and then cried."

The researchers studied DNA gathered as part of the Collaborative Study on the Genetics of Alcoholism (COGA). In this multi-center study, people who have been treated for alcohol dependence and members of their families provide DNA samples to researchers, who isolated DNA regions related to alcohol abuse and dependence, as well as a variety of other outcomes.

Some of the participants in the study also took the Wechsler Adult Intelligence Scale-Revised, a traditional IQ test. In all, members of 200 families, including more than 2,150 individuals, took the Wechsler test, and those results were matched to differences in individuals' DNA.

By comparing individual differences embedded in DNA, the team zeroed in on CHRM2, the neuronal receptor gene on chromosome 7. The CHRM2 gene activates a multitude of signaling pathways in the brain involved in learning, memory and other higher brain functions. The research team doesn't yet understand how the gene exerts its effects on intelligence.

Intelligence was one of the first traits that attracted the attention of people interested in the interplay of genes and environmental influences. Early studies of adopted children, for example, showed that when children grow up away from their biological parents, their IQs are more closely correlated to biological parents, with whom they share genes, than adoptive parents, with whom they share an environment.

But in spite of the association between genes and intelligence, it has been difficult to find specific variations that influence intelligence. The genes identified in the past were those that had profoundly negative effects on intelligence - genes that cause mental retardation, for example. Those that contribute to less dramatic differences have been much harder to isolate.

Dick's team is not the first to notice a link between intelligence and the CHRM2 gene. In 2003, a group in Minnesota looked at a single marker in the gene and noted that the variation was related to an increase in IQ. A more recent Dutch study looked at three regions of DNA along the gene and also noticed influences on intelligence. In this new study, however, researchers tested multiple genetic markers throughout the gene.

"If we look at a single marker, a DNA variation might influence IQ scores between two and four points, depending on which variant a person carries," Dick explains. "We did that all up and down the gene and found that the variations had cumulative effects, so that if one person had all of the 'good' variations and another all of the 'bad' variations, the difference in IQ might be 15 to 20 points. Unfortunately, the numbers of people at those extremes were so small that the finding isn't statistically significant, but the point is we saw fairly substantial differences in our sample when we combined information across multiple regions of the gene."

Dick says the next step is to look at the gene and its numerous variants to learn what is going on biologically that might affect cognitive performance. Presently, she says it's too early to predict how small changes in the gene might be influencing communication in the brain to affect intelligence, and she says it's nearly certain CHRM2 is not the only gene involved.

"Perhaps as many as 100 genes or more could influence intelligence," she says. "I think all of the genes involved probably have small, cumulative effects on increasing or decreasing I.Q., and I expect overall intelligence is a function of the accumulation of all of these genetic variants, not to mention environmental influences ranging from socio-economic status to the value that's placed on learning when children are growing up."

The cholinergic neurotransmitter system is thought to be involved in many aspects of memory, attention, and higher cognition. In the Collaborative Study on the Genetics of Alcoholism (COGA) sample, we have previously reported linkage and association to the cholinergic muscarinic 2 receptor gene (CHRM2) on chromosome 7 with evoked EEG oscillations (Jones et al. 2004), providing evidence that this gene may be involved in human brain dynamics and cognition. In addition, a small number of genetic markers were genotyped in CHRM2 in the Minnesota Twin and Family Study (Comings et al. 2003) and a Dutch family study (Gosso et al. 2006, in press) and both research groups found evidence that this gene may be involved in intelligence. In the COGA sample, we have extensively genotyped SNPs (single nucleotide polymorphisms) within and flanking the CHRM2 gene. We find evidence of association with multiple SNPs across CHRM2 and Performance IQ, as measured by the Wechsler Adult Intelligence Scale-Revised (WAIS-R). These results remain significant after taking into account alcohol dependence and depression diagnoses in the sample.

Wednesday, February 28, 2007

Study: Early Europeans unable to stomach milk

The first direct evidence that early Europeans were unable to digest milk has been found by scientists at UCL (University College London) and Mainz University.

In a study, published in the journal PNAS [1] (Proceedings of the National Academy of Sciences), the team shows that the gene that controls our ability to digest milk was missing from Neolithic skeletons dating to between 5840 and 5000 BC. However, through exposure to milk, lactose tolerance evolved extremely rapidly, in evolutionary terms (see lactose intolerance). Today, it is present in over ninety per cent of the population of northern Europe and is also found in some African and Middle Eastern populations but is missing from the majority of the adult population globally.

Dr Mark Thomas, UCL Biology, said: "The ability to drink milk is the most advantageous trait that's evolved in Europeans in the recent past. Without the enzyme lactase, drinking milk in adulthood causes bloating and diarrhoea. Although the benefits of milk tolerance are not fully understood yet, they probably include: the continuous supply of milk compared to the boom and bust of seasonal crops; its nourishing qualities; and the fact that it's uncontaminated by parasites, unlike stream water, making it a safer drink. All in all, the ability to drink milk gave some early Europeans a big survival advantage."

The team carried out DNA tests on Neolithic skeletons from some of the earliest organised farming communities in Europe. Their aim was to find out whether these early Europeans from various sites in central, northeast and southeast Europe, carried a version of the lactase gene that controls our ability to produce the essential enzyme lactase into adulthood. The team found that it was absent from their ancient bone DNA. This led the researchers to conclude that the consumption and tolerance of milk would have been very rare or absent at the time.

Scientists have known for decades that at some point in the past all humans were lactose intolerant. What was not known was just how recently lactose tolerance evolved.

Dr Thomas said: "To go from lactose tolerance being rare or absent seven to eight thousand years ago to the commonality we see today in central and northern Europeans just cannot be explained by anything except strong natural selection. Our study confirms that the variant of the lactase gene appeared very recently in evolutionary terms and that it became common because it gave its carriers a massive survival advantage. Scientists have inferred this already through analysis of genes in today's population but we've confirmed it by going back and looking at ancient DNA."

This study challenges the theory that certain groups of Europeans were lactose tolerant and that this inborn ability led the community to pursue dairy farming. Instead, they actually evolved their tolerance of milk within the last 8000 years due to exposure to milk.

Dr Thomas said: "There were two theories out there: one that lactose tolerance led to dairy farming and another that exposure to milk led to the evolution of lactose tolerance. This is a simple chicken or egg question but one that is very important to archaeologists, anthropologists and evolutionary biologists. We found that the lactose tolerance variant of the lactase gene only became common after dairy farming, which started around 9 thousand years ago in Europe.

"This is just one part of the picture researchers are gathering about lactose tolerance and the origins of Europeans. Next on the list is why there is such disparity in lactose tolerance between populations. It's striking, for example, that today around eighty per cent of southern Europeans cannot tolerate lactose even though the first dairy farmers in Europe probably lived in those areas. Through computer simulations and DNA testing we are beginning to get glimpses of the bigger early European picture."

Lactase persistence (LP), the dominant Mendelian trait conferring the ability to digest the milk sugar lactose in adults, has risen to high frequency in central and northern Europeans in the last 20,000 years. This trait is likely to have conferred a selective advantage in individuals who consume appreciable amounts of unfermented milk. Some have argued for the "culture-historical hypothesis," whereby LP alleles were rare until the advent of dairying early in the Neolithic but then rose rapidly in frequency under natural selection. Others favor the "reverse cause hypothesis," whereby dairying was adopted in populations with preadaptive high LP allele frequencies. Analysis based on the conservation of lactase gene haplotypes indicates a recent origin and high selection coefficients for LP, although it has not been possible to say whether early Neolithic European populations were lactase persistent at appreciable frequencies. We developed a stepwise strategy for obtaining reliable nuclear ancient DNA from ancient skeletons, based on (i) the selection of skeletons from archaeological sites that showed excellent biomolecular preservation, (ii) obtaining highly reproducible human mitochondrial DNA sequences, and (iii) reliable short tandem repeat (STR) genotypes from the same specimens. By applying this experimental strategy, we have obtained high-confidence LP-associated genotypes from eight Neolithic and one Mesolithic human remains, using a range of strict criteria for ancient DNA work. We did not observe the allele most commonly associated with LP in Europeans, thus providing evidence for the culture-historical hypothesis, and indicating that LP was rare in early European farmers.

Primate evolution is a central topic in biology and much information can be obtained from DNA sequence data. A key parameter is the time "when we became human," i.e., the time in the past when descendents of the human-chimp ancestor split into human and chimpanzee. Other important parameters are the time in the past when descendents of the human-chimp-gorilla ancestor split into descendents of the human-chimp ancestor and the gorilla ancestor, and population sizes of the human-chimp and human-chimp-gorilla ancestors. To estimate speciation times and ancestral population sizes we have developed a new methodology that explicitly utilizes the spatial information in contiguous genome alignments. Furthermore, we have applied this methodology to four long autosomal human-chimp-gorilla-orangutan alignments and estimated a very recent speciation time of human and chimp (around 4 million years) and ancestral population sizes much larger than the present-day human effective population size. We also analyzed X-chromosome sequence data and found that the X chromosome has experienced a different history from that of autosomes, possibly because of selection.

The genealogical relationship of human, chimpanzee, and gorilla varies along the genome. We develop a hidden Markov model (HMM) that incorporates this variation and relate the model parameters to population genetics quantities such as speciation times and ancestral population sizes. Our HMM is an analytically tractable approximation to the coalescent process with recombination, and in simulations we see no apparent bias in the HMM estimates. We apply the HMM to four autosomal contiguous human-chimp-gorilla-orangutan alignments comprising a total of 1.9 million base pairs. We find a very recent speciation time of human-chimp (4.1 plus/minus 0.4 million years), and fairly large ancestral effective population sizes (65,000 plus/minus 30,000 for the human-chimp ancestor and 45,000 plus/minus 10,000 for the human-chimp-gorilla ancestor). Furthermore, around 50% of the human genome coalesces with chimpanzee after speciation with gorilla. We also consider 250,000 base pairs of X-chromosome alignments and find an effective population size much smaller than 75% of the autosomal effective population sizes. Finally, we find that the rate of transitions between different genealogies correlates well with the region-wide present-day human recombination rate, but does not correlate with the fine-scale recombination rates and recombination hot spots, suggesting that the latter are evolutionarily transient.

Introduction

The recent evolutionary history of the human species can be investigated by comparative approaches using the genomes of the great apes: chimpanzee, gorilla, and orangutan. Nucleotide differences, accumulated by fixation of mutations, carry a wealth of information on important issues such as speciation times, properties of ancestral species (e.g., population sizes), and how speciation occurred. Genes or genomic fragments with unusual patterns of nucleotide differences and divergence may have been under strong natural selection during recent evolution of the human species. Sequence analyses can also aid interpretations of the incomplete primate fossil records and aid assignment of dated fossils to evolutionary lineages. For instance, it is still debated whether the Millennium man, Orrorin tugenensis, which has been dated to 6 million years (Myr) ago, and Sahelanthropus tchadensis, which has been dated to 6-7 Myr ago, belong to the human lineage or the human-chimp (HC) lineage.

Comparative analyses of multiple alignments of small fragments of human, chimpanzee, gorilla, and orangutan sequence have revealed that the human genome is more similar to the gorilla genome than to the chimpanzee genome for a considerable fraction of single genes. Such a conflict between species and gene genealogy is expected if the time span between speciation events is small measured in the number of 2N generations, where N is the effective population of the ancestral species (see Figure 1). In that case, N can be estimated from the proportion of divergent genealogies if one assumes that speciation is an instantaneous event. Indeed, this has been done in several studies that find a HC ancestral effective population size NHC of 2-10 times the human present-day effective population size NH = 10,000. Recently, Patterson et al. studied a very large number of small human-chimp-gorilla-orangutan-macaque alignments. They found, in agreement with O'hUigin et al., that a large proportion of sites supporting alternative genealogies are caused by hypermutability and that the fraction of the genome with alternative genealogies therefore has been overestimated in previous studies. After using a statistical correction for substitution rate heterogeneity, Patterson et al. found that the variance in coalescence times is too large to be accounted for by instant speciation and a large ancestral effective population size, and that the speciation process therefore must have been complex. Particularly, the X chromosome shows a deviant pattern, which also led them to conclude that HC gene flow ceased and final speciation occurred as recently as 4 Myr ago. This date is generally believed to be the most recent time compatible with the fossil record, if the Millennium man and Sahelanthropus are not on the human lineage.

Whole genome sequences of gorilla and orangutan will soon supplement the already available whole genome sequences of human and chimpanzee. These four genomes are so closely related that alignments of large contiguous parts of the genomes can be constructed. Analysis of such large fragments is challenging because different parts of the alignment will have different evolutionary histories (and thus different genealogies, see Figure 1) because of recombination. Ideally, one would like to infer the genealogical changes directly from the data and then analyze each type of genealogy separately. A natural approach to this challenge is to move along the alignment, and simultaneously compute the probabilities of different relationships and speciation times. While recombination has been considered in previous likelihood models, the spatial information along the alignment has largely been ignored.

In this paper we describe a hidden Markov model (HMM) that allows the presence of different genealogies along large multiple alignments. The hidden states are different possible genealogies (labeled HC1, HC2, HG, and CG in Figures 1 and 2). Parameters of the HMM include population genetics parameters such as the HC and human-chimp-gorilla (HCG) ancestral effective population sizes, NHC and NHCG, and speciation times tau1 and tau2 (see Figure 1). We therefore name our approach a coalescent HMM (coal-HMM). The statistical framework of HMMs yields parameter estimates with associated standard errors, and posterior probabilities of hidden states. We show by simulation studies that the coal-HMM recovers parameters from the coalescence with recombination process, and we apply the coal-HMM to five long contiguous human-chimp-gorilla-orangutan (HCGO) alignments obtained from the NIH Intramural Sequencing Center comparative sequencing program (Targets 1, 106, 121, and 122 on four different autosomes and Target 46 on the X chromosome). We consistently find very recent estimates of HC speciation times and a large variance in the time to common ancestry along the genome. Similar to Patterson et al., we find that the X chromosome has a smaller effective population size than expected. The mapping of genealogical states further allows us to correlate transitions in genealogies with properties of the genome, and here we focus on fine-scale and region-wide recombination rate estimates.

Saturday, February 24, 2007

Reporting findings that help shape our understanding of how tool use has evolved among primates, researchers have discovered evidence that chimpanzees, at least under some conditions, are capable of habitually fashioning and using tools to hunt mammalian prey. The work [1], reported by Jill Pruetz of Iowa State University and Paco Bertolani of the University of Cambridge, will appear online in the journal Current Biology on February 22nd 2007.

Chimpanzees are well known for their ingenuity in using tools for some tasks, such as obtaining invertebrate insects from logs or pounding open hard nuts, but there had been only fleeting evidence of chimpanzees brandishing tools for bona fide hunting.

In the new work, researchers observed tool use in hunting by the Fongoli community of savanna-dwelling chimpanzees (Pan troglodytes verus) in southeastern Senegal. Chimpanzees were observed making spear-like tools in a step-wise fashion, and subsequently using them with jabbing motions in an apparent effort to obtain lesser bushbabies (Galago senegalensis) from cavities in hollow branches or tree trunks. Bushbabies are nocturnal prosimians that retire to such hidden cavities during the day.

Although there was only one successful attempt in 22 recorded instances of the chimpanzees using the spear-like tools to find and obtain prey, the researchers observed that tool-crafting and associated hunting behavior was systematic and consistent, suggesting that it was habitual. The hunting behavior included forceful jabbing motions into branch or trunk hollows, and chimpanzees were seen to subsequently open the hollows by breaking wood off from a distance, suggesting that the jabbing actions were intended to immobilize bushbabies, rather than rouse them from their cavities (bushbabies move quickly and might otherwise easily evade chimpanzees once roused).

Two notable aspects of the behavior observed in the Fongoli group were that on the one hand, it is rare for chimpanzees to consume prosimian prey - in other study sites, red colobus monkeys, hunted mainly by males, are the chimps' most common prey - and on the other hand, the tool use appeared to be primarily restricted to females and immature individuals. These two behavior characteristics could both be related to the fact that the Fongoli community inhabits a mosaic savannah that is relatively dry, and where red colobus monkeys are absent. This habitat may promote efforts - such as the observed tool use - to obtain meat through other means.

The authors point out that the females and immature chimpanzees using the spear-like tools appear to be exploiting a niche relatively ignored by males, an observation that supports a previous hypothesis that female hominids played a role in the evolution of the earliest tool technology and suggests that this technology may have included tools for hunting. [Primatology, Anthropology]

Although tool use is known to occur in species ranging from naked mole rats [1] to owls [2], chimpanzees are the most accomplished tool users [3, 4, 5]. The modification and use of tools during hunting, however, is still considered to be a uniquely human trait among primates. Here, we report the first account of habitual tool use during vertebrate hunting by nonhumans. At the Fongoli site in Senegal, we observed ten different chimpanzees use tools to hunt prosimian prey in 22 bouts. This includes immature chimpanzees and females, members of age-sex classes not normally characterized by extensive hunting behavior. Chimpanzees made 26 different tools, and we were able to recover and analyze 12 of these. Tool construction entailed up to five steps, including trimming the tool tip to a point. Tools were used in the manner of a spear, rather than a probe or rousing tool. This new information on chimpanzee tool use has important implications for the evolution of tool use and construction for hunting in the earliest hominids, especially given our observations that females and immature chimpanzees exhibited this behavior more frequently than adult males.

In the early 1960s, when the british primatologist Jane Goodall first observed wild chimpanzees hunting and eating meat in Gombe National Park, Tanzania, it was widely believed that these animals were strict vegetarians. Skeptics suggested that the diet of the Gombe chimpanzees was aberrant. Others suggested that the quantity of meat the chimpanzees ate was trivial. After more than 30 years of research, however, it is now clear that meat is a natural part of the chimpanzees' diet. Indeed, hunting has been observed at most of the other sites where chimpanzees are studied across central Africa. And, it turns out, a chimpanzee community may eat several hundred kilograms of meat in a single year.

To many anthropologists this is a surprising development. Of all the higher primates, only human beings and chimpanzees hunt and eat meat on a regular basis. The similarities pose an intriguing prospect: Might the close evolutionary relationship between chimpanzees and human beings provide some clues to the evolution of our own behavior? We do know that the earliest bipedal hominids, the australopithecines, evolved in Africa about 5 million years ago and that they shared a common ancestor with modern chimpanzees shortly before that time. Unfortunately, the evidence for the occurrence of meat-eating among the early australopithecines is spotty at best. Primitive stone tools that were made 2.5 million years ago suggest that early hominids had the means to carve the flesh from large carcasses, but we know very little about their diets before that time. Were they hunters or perhaps, as many anthropologists now argue, scavengers? The behavior of chimpanzees may provide a window through which we can see much that has been lost in the fossil record.

There are also some interesting subtleties to the chimpanzees' hunting behavior that need to be addressed. Although chimpanzees can and do hunt alone, they often form large hunting parties consisting of more than 10 adult males, plus females and juveniles. Chimpanzees also go on "hunting binges" in which they kill a large number of monkeys and other animals over a period of several days or weeks. Such binges have always been a little mysterious. What could incite a chimpanzee to suddenly forgo plant foraging and turn to hunting? Are there social or ecological factors associated with the impetus to hunt? What ecological effects does the chimpanzees' predatory behavior have on their prey?

In the past five years I have been mindful of such questions as I observed the chimpanzees and their primary prey at Gombe, the red colobus monkey. Although we are only beginning to understand some of the causes and consequences of the chimpanzees' actions, what we have discovered is more complicated and more interesting than anyone suspected. For chimpanzees, meat is not only another way to get nutrients like fat and protein, but a means to make political bonds and gain access to sexually receptive females.

David Attenborough video clip* showing how hunting chimpanzees co-ordinate their behavior in order to trap and kill (then eat) a colobus monkey:

*From The Trials of Life: A Natural History of Behaviour, a BBC nature documentary first broadcast in 1990

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The video footage below hasn't any commentary but is accompanied by the following text by kambizkamrani: "Adolescent female Tumbo isolates a potential spear and modifies it. She begins to jab it into a tree to spear her prey. She then climbs the tree and begins jumping on the large limb, which eventually breaks off, allowing her to reach in and retrieve the prey, a bushbaby (Galago senegalensis)." - watching the National Geographic video "Video: Chimps Make and Use 'Spears' to Hunt" first may help.

What is wrong with intelligent design?

In a thought-provoking paper from the March 2007 issue of The Quarterly Review of Biology , Elliott Sober (University of Wisconsin) clearly discusses the problems with two standard criticisms of intelligent design: that it is unfalsifiable and that the many imperfect adaptations found in nature refute the hypothesis of intelligent design.

Biologists from Charles Darwin to Stephen Jay Gould have advanced this second type of argument. Stephen Jay Gould's well-known example of a trait of this type is the panda's thumb. If a truly intelligent designer were responsible for the panda, Gould argues, it would have provided a more useful tool than the stubby proto-thumb that pandas use to laboriously strip bamboo in order to eat it.

ID proponents have a ready reply to this objection. We do not know whether an intelligent designer intended for pandas to be able to efficiently strip bamboo. The "no designer worth his salt" argument assumes the designer would want pandas to have better eating implements, but the objection has no justification for this assumption. In addition, Sober points out, this criticism of ID also concedes that creationism is testable.

A second common criticism of ID is that it is untestable. To develop this point, scientists often turn to the philosopher Karl Popper's idea of falsifiability. According to Popper, a scientific statement must allow the possibility of an observation that would disprove it. For example, the statement "all swans are white" is falsifiable, since observing even one swan that isn't white would disprove it. Sober points out that this criterion entails that many ID statements are falsifiable; for example, the statement that an intelligent designer created the vertebrate eye entails that vertebrates have eyes, which is an observation.

This leads Sober to jettison the concept of falsifiability and to provide a different account of testability. "If ID is to be tested," he says, "it must be tested against one or more competing hypotheses." If the ID claim about the vertebrate eye is to be tested against the hypothesis that the vertebrate eye evolved by Darwinian processes, the question is whether there is an observation that can discriminate between the two. The observation that vertebrates have eyes cannot do this.

Sober also points out that criticism of a competing theory, such as evolution, is not in-and-of-itself a test of ID. Proponents of ID must construct a theory that makes its own predictions in order for the theory to be testable. To contend that evolutionary processes cannot produce "irreducibly complex" adaptations merely changes the subject, Sober argues.

"When scientific theories compete with each other, the usual pattern is that independently attested auxiliary propositions allow the theories to make predictions that disagree with each other," Sober writes. "No such auxiliary propositions allow … ID to do this." In developing this idea, Sober makes use of ideas that the French philosopher Pierre Duhem developed in connection with physical theories - theories usually do not, all by themselves, make testable predictions. Rather, they do so only when supplemented with auxiliary information. For example, the laws of optics do not, by themselves, predict when eclipses will occur; they do so when independently justified claims about the positions of the earth, moon, and sun are taken into account.

Similarly, ID claims make predictions when they are supplemented by auxiliary claims. The problem is that these auxiliary assumptions about the putative designer's goals and abilities are not independently justified. Surprisingly, this is a point that several ID proponents concede.

This article reviews two standard criticisms of creationism/intelligent design (ID): it is unfalsifiable, and it is refuted by the many imperfect adaptations found in nature. Problems with both criticisms are discussed. A conception of testability is described that avoids the defects in Karl Popper's falsifiability criterion. Although ID comes in multiple forms, which call for different criticisms, it emerges that ID fails to constitute a serious alternative to evolutionary theory.

In this hour of Science Friday, we'll look at a collection of topics centered around evolution, creationism, and education. First, we'll take a look back at the Dover, Pennsylvania evolution trial. The judge's (John E. Jones III) ruling in that case dealt a blow to one district's plans to bring "intelligent design" to its public school science classes. We'll talk with the Pulitzer Prize winning author (Edward Humes) of a new book on the trial.

We'll also talk with the director (Randy Olson) of "A Flock of Dodos," a new film that tackles the question of why scientists can't seem to get the intelligent design debate to go away. Plus, an update on the nationwide battle over teaching creationism in public schools. Did the fall elections bring any changes to policies in science education battlegrounds such as Kansas?